Re: [gmx-users] Problem with mpirun
Hi, Can you send us the output of gmx_mpi --version? I typically see illegal instructions when I compile gromacs on one architecture but accidentally try to run it on another. Kevin On Thu, Feb 6, 2020 at 6:38 AM Seketoulie Keretsu wrote: > Dear Sir/Madam, > > We just installed gromacs 2019 today (MPI compiled) and we're currently > testing the commands with MPI. The installations went fine however,we are > having issues with the commands. > > $ echo $PATH > /opt/vmd/1.9.3/bin:/opt/g_mmpbsa/bin:/opt/gromacs/2019.5/bin > > However, when we execute the commands we get the following response. > > mpirun -np 8 gmx_mpi mdrun -s md_0_10.tpr -o md_0_10.trr -cpi md_0_10.cpt > -c md_0_10.gro -e md_0_10.edr -g md_0_10.log > > > === > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = RANK 15 PID 23681 RUNNING AT biopo1 > = KILLED BY SIGNAL: 4 (Illegal instruction) > > === > > We get the same error for 'mpirun -np 16 gmx_mpi mdrun -h' or ' mpirun -np > 8 gmx_mpi mdrun -v -deffnm md_0_10' > > What are we missing here, please advise. > > Sincerely, > Seket > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with mpirun
Dear Sir/Madam, We just installed gromacs 2019 today (MPI compiled) and we're currently testing the commands with MPI. The installations went fine however,we are having issues with the commands. $ echo $PATH /opt/vmd/1.9.3/bin:/opt/g_mmpbsa/bin:/opt/gromacs/2019.5/bin However, when we execute the commands we get the following response. mpirun -np 8 gmx_mpi mdrun -s md_0_10.tpr -o md_0_10.trr -cpi md_0_10.cpt -c md_0_10.gro -e md_0_10.edr -g md_0_10.log === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 15 PID 23681 RUNNING AT biopo1 = KILLED BY SIGNAL: 4 (Illegal instruction) === We get the same error for 'mpirun -np 16 gmx_mpi mdrun -h' or ' mpirun -np 8 gmx_mpi mdrun -v -deffnm md_0_10' What are we missing here, please advise. Sincerely, Seket -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with MPIRUN and Ewald
Actually I have to make a correction, the .log file doesn't say anything. Da: Matteo Busato Inviato: giovedì 23 febbraio 2017 10.34.52 A: gromacs.org_gmx-users@maillist.sys.kth.se Oggetto: Problem with MPIRUN and Ewald Good morning to everyone, I am trying to perform a simple classical dynamic of a box of 500 TIP3P water molecules with an Ag+ ion in its center. However, when running the dynamic with 8 physical cores but no multithread with mpirun it crashes and the output of the job reports: "The number of PME grid lines per rank along x is 3. But when using OpenMP threads, the number of grid lines per rank along x should be > = pme_order (6) or pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly more along y and/or z) by specifyng -dd manually" The md.log file says instead: "Fatal error: the size of the domain decomposition grid (125) does not match the number of ranks (8). The total number of ranks is 8". The strange fact is that it works on supercomputer CINECA resources but it doesn't on our local cluster. This is the .mdp file I'm using: ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 50 ; 1 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t= 1.0 ref_t= 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state012345678910 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 ; We are not transforming any bonded or restrained interactions bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = AG ; name of moleculetype to decouple couple-lambda0 = none ; no interactions at lambda=0 couple-lambda1 = vdw-q; turn on both vdW and Coulomb couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Thank you in advance for your
[gmx-users] Problem with MPIRUN and Ewald
Good morning to everyone, I am trying to perform a simple classical dynamic of a box of 500 TIP3P water molecules with an Ag+ ion in its center. However, when running the dynamic with 8 physical cores but no multithread with mpirun it crashes and the output of the job reports: "The number of PME grid lines per rank along x is 3. But when using OpenMP threads, the number of grid lines per rank along x should be > = pme_order (6) or pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly more along y and/or z) by specifyng -dd manually" The md.log file says instead: "Fatal error: the size of the domain decomposition grid (125) does not match the number of ranks (8). The total number of ranks is 8". The strange fact is that it works on supercomputer CINECA resources but it doesn't on our local cluster. This is the .mdp file I'm using: ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 50 ; 1 ns nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t= 1.0 ref_t= 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state012345678910 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 ; We are not transforming any bonded or restrained interactions bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Masses are not changing (particle identities are the same at lambda = 0 and lambda = 1) mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = AG ; name of moleculetype to decouple couple-lambda0 = none ; no interactions at lambda=0 couple-lambda1 = vdw-q; turn on both vdW and Coulomb couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Thank you in advance for your suggestions. Matteo Busato -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
